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- PDB-7p87: Crystal structure of YTHDC1 with compound YLI_DC1_001 -

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Basic information

Entry
Database: PDB / ID: 7p87
TitleCrystal structure of YTHDC1 with compound YLI_DC1_001
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / Inhibitor / complex / m6A
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
Chem-ID0 / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBedi, R.K. / Li, Y. / Dolbois, A. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: Eur J Med Chem Rep / Year: 2022
Title: Structure-based design of ligands of the m6A-RNA reader YTHDC1
Authors: Li, Y. / Bedi, R.K. / Nai, F. / von Roten, V. / Dolbois, A. / Zalesak, F. / Nachawati, R. / Huang, D. / Caflisch, A.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 16, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
SupersessionApr 6, 2022ID: 6YM7
Revision 2.1Apr 6, 2022Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 2.2Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing protein 1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,96511
Polymers41,9342
Non-polymers1,0319
Water10,863603
1
A: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4355
Polymers20,9671
Non-polymers4674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5316
Polymers20,9671
Non-polymers5635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.780, 103.780, 42.180
Angle α, β, γ (deg.)90.000, 105.555, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B


Mass: 20967.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MU7
#2: Chemical ChemComp-ID0 / N-methyl-4,5,6,7-tetrahydro-1H-indazole-3-carboxamide


Mass: 179.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2M Ammonium Sulphate, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→40.64 Å / Num. obs: 78147 / % possible obs: 96.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 13.48 Å2 / CC1/2: 1 / Net I/σ(I): 17.04
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 12188 / CC1/2: 0.697

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H

4r3h


Resolution: 1.3→40.64 Å / SU ML: 0.1409 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 3903 5 %
Rwork0.1812 74132 -
obs0.1824 78035 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.64 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 61 603 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582754
X-RAY DIFFRACTIONf_angle_d0.8543755
X-RAY DIFFRACTIONf_chiral_restr0.08406
X-RAY DIFFRACTIONf_plane_restr0.0062471
X-RAY DIFFRACTIONf_dihedral_angle_d9.7658381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.29491300.29582469X-RAY DIFFRACTION89.9
1.32-1.330.30081360.28432577X-RAY DIFFRACTION94.69
1.33-1.350.29981350.27142570X-RAY DIFFRACTION94.98
1.35-1.370.25071380.26392613X-RAY DIFFRACTION95.09
1.37-1.390.24151360.2462581X-RAY DIFFRACTION95.3
1.39-1.410.22951360.24342601X-RAY DIFFRACTION95.4
1.41-1.430.24661370.2432587X-RAY DIFFRACTION95.68
1.43-1.460.26411390.23692656X-RAY DIFFRACTION96.05
1.46-1.480.25611370.23432589X-RAY DIFFRACTION95.88
1.48-1.510.2711390.21092648X-RAY DIFFRACTION96.3
1.51-1.540.21391370.19912609X-RAY DIFFRACTION96.49
1.54-1.570.22451380.19342624X-RAY DIFFRACTION96.51
1.57-1.60.24381400.1942652X-RAY DIFFRACTION96.71
1.6-1.640.22491380.18682623X-RAY DIFFRACTION97.15
1.64-1.680.18921410.18192672X-RAY DIFFRACTION97.23
1.68-1.730.22131400.18652668X-RAY DIFFRACTION97.64
1.73-1.780.21421410.18882668X-RAY DIFFRACTION97.53
1.78-1.830.2321400.19492675X-RAY DIFFRACTION97.78
1.83-1.90.19341410.17812669X-RAY DIFFRACTION97.98
1.9-1.980.18641410.17512674X-RAY DIFFRACTION97.98
1.98-2.070.20091400.16552667X-RAY DIFFRACTION98.18
2.07-2.170.18241420.16872693X-RAY DIFFRACTION98.44
2.17-2.310.21231410.17342689X-RAY DIFFRACTION98.43
2.31-2.490.23111440.17812737X-RAY DIFFRACTION99.04
2.49-2.740.21961410.18442681X-RAY DIFFRACTION98.81
2.74-3.140.21121440.17422724X-RAY DIFFRACTION99.38
3.14-3.950.18291450.15252751X-RAY DIFFRACTION99.62
3.95-40.640.16181460.15982765X-RAY DIFFRACTION99.39

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